Starting phenix.real_space_refine
on Thu Jul 24 09:23:58 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uet_64091/07_2025/9uet_64091.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      4      5.21       5
     S      42      5.16       5
     C    3940      2.51       5
     N     906      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5906
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2899
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 14, 'TRANS': 353}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {' MG': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.59, per 1000 atoms: 1.29
  Number of scatterers: 5906
  At special positions: 0
  Unit cell: (90.95, 112.35, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       2     15.00
     Mg      4     11.99
     O    1012      8.00
     N     906      7.00
     C    3940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.96
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      73.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 32
    Processing helix  chain 'A' and resid 43 through 55
      removed outlier: 4.416A  pdb=" N   LEU A  48 " --> pdb=" O   PRO A  44 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   TYR A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 85
    Processing helix  chain 'A' and resid 93 through 118
      removed outlier: 3.747A  pdb=" N   TYR A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 151
      removed outlier: 4.092A  pdb=" N   SER A 137 " --> pdb=" O   HIS A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 155
      removed outlier: 3.847A  pdb=" N   THR A 155 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 152 through 155'
    Processing helix  chain 'A' and resid 156 through 180
      removed outlier: 4.070A  pdb=" N   SER A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   PHE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 208
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 226 through 248
      removed outlier: 4.060A  pdb=" N   VAL A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 285
      removed outlier: 4.144A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 293
      removed outlier: 3.946A  pdb=" N   LYS A 292 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 318
    Processing helix  chain 'A' and resid 326 through 328
      No H-bonds generated for 'chain 'A' and resid 326 through 328'
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 3.758A  pdb=" N   LEU A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 377
    Processing helix  chain 'B' and resid 22 through 32
    Processing helix  chain 'B' and resid 43 through 55
      removed outlier: 4.417A  pdb=" N   LEU B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   TYR B  49 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 85
    Processing helix  chain 'B' and resid 93 through 118
      removed outlier: 3.746A  pdb=" N   TYR B  97 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 151
      removed outlier: 4.092A  pdb=" N   SER B 137 " --> pdb=" O   HIS B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 155
      removed outlier: 3.847A  pdb=" N   THR B 155 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 152 through 155'
    Processing helix  chain 'B' and resid 156 through 180
      removed outlier: 4.070A  pdb=" N   SER B 164 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   PHE B 171 " --> pdb=" O   GLY B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 208
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 226 through 248
      removed outlier: 4.060A  pdb=" N   VAL B 246 " --> pdb=" O   ASN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 285
      removed outlier: 4.144A  pdb=" N   ILE B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER B 285 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 293
      removed outlier: 3.945A  pdb=" N   LYS B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 318
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 329 through 341
      removed outlier: 3.759A  pdb=" N   LEU B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 377

    392 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 3.48 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 878
        1.31 -     1.43: 1748
        1.43 -     1.56: 3370
        1.56 -     1.68: 6
        1.68 -     1.81: 64
  Bond restraints: 6066
  Sorted by residual:
  bond pdb=" N   PRO A 126 "
       pdb=" CD  PRO A 126 "
    ideal  model  delta    sigma   weight residual
    1.473  1.546 -0.073 1.40e-02 5.10e+03 2.73e+01
  bond pdb=" N   PRO B 126 "
       pdb=" CD  PRO B 126 "
    ideal  model  delta    sigma   weight residual
    1.473  1.546 -0.073 1.40e-02 5.10e+03 2.73e+01
  bond pdb=" CA  PRO B 126 "
       pdb=" C   PRO B 126 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 9.50e-03 1.11e+04 2.34e+01
  bond pdb=" CA  PRO A 126 "
       pdb=" C   PRO A 126 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 9.50e-03 1.11e+04 2.34e+01
  bond pdb=" C31 POV B 501 "
       pdb=" O31 POV B 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.420 -0.093 2.00e-02 2.50e+03 2.16e+01
  ... (remaining 6061 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.74: 8120
        4.74 -     9.48: 88
        9.48 -    14.22: 29
       14.22 -    18.95: 3
       18.95 -    23.69: 6
  Bond angle restraints: 8246
  Sorted by residual:
  angle pdb=" N   ASN A 343 "
        pdb=" CA  ASN A 343 "
        pdb=" C   ASN A 343 "
      ideal   model   delta    sigma   weight residual
     109.96   89.88   20.08 1.50e+00 4.44e-01 1.79e+02
  angle pdb=" N   ASN B 343 "
        pdb=" CA  ASN B 343 "
        pdb=" C   ASN B 343 "
      ideal   model   delta    sigma   weight residual
     109.96   89.91   20.05 1.50e+00 4.44e-01 1.79e+02
  angle pdb=" N   THR A 121 "
        pdb=" CA  THR A 121 "
        pdb=" C   THR A 121 "
      ideal   model   delta    sigma   weight residual
     109.81   90.30   19.51 1.53e+00 4.27e-01 1.63e+02
  angle pdb=" N   THR B 121 "
        pdb=" CA  THR B 121 "
        pdb=" C   THR B 121 "
      ideal   model   delta    sigma   weight residual
     109.81   90.30   19.51 1.53e+00 4.27e-01 1.63e+02
  angle pdb=" C   GLN A 117 "
        pdb=" CA  GLN A 117 "
        pdb=" CB  GLN A 117 "
      ideal   model   delta    sigma   weight residual
     109.95   86.26   23.69 1.99e+00 2.53e-01 1.42e+02
  ... (remaining 8241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.07: 3123
       20.07 -    40.13: 323
       40.13 -    60.20: 52
       60.20 -    80.27: 4
       80.27 -   100.33: 2
  Dihedral angle restraints: 3504
    sinusoidal: 1368
      harmonic: 2136
  Sorted by residual:
  dihedral pdb=" C   GLN A 117 "
           pdb=" N   GLN A 117 "
           pdb=" CA  GLN A 117 "
           pdb=" CB  GLN A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -97.65  -24.95     0      2.50e+00 1.60e-01 9.96e+01
  dihedral pdb=" C   GLN B 117 "
           pdb=" N   GLN B 117 "
           pdb=" CA  GLN B 117 "
           pdb=" CB  GLN B 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -97.68  -24.92     0      2.50e+00 1.60e-01 9.94e+01
  dihedral pdb=" C   ASN A 122 "
           pdb=" N   ASN A 122 "
           pdb=" CA  ASN A 122 "
           pdb=" CB  ASN A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.14  -18.46     0      2.50e+00 1.60e-01 5.45e+01
  ... (remaining 3501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 841
       0.088 -    0.175: 91
       0.175 -    0.263: 4
       0.263 -    0.351: 2
       0.351 -    0.438: 6
  Chirality restraints: 944
  Sorted by residual:
  chirality pdb=" CA  ASN A 122 "
            pdb=" N   ASN A 122 "
            pdb=" C   ASN A 122 "
            pdb=" CB  ASN A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.95   -0.44 2.00e-01 2.50e+01 4.80e+00
  chirality pdb=" CA  ASN B 122 "
            pdb=" N   ASN B 122 "
            pdb=" C   ASN B 122 "
            pdb=" CB  ASN B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.95   -0.44 2.00e-01 2.50e+01 4.80e+00
  chirality pdb=" CA  SER A 125 "
            pdb=" N   SER A 125 "
            pdb=" C   SER A 125 "
            pdb=" CB  SER A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.35e+00
  ... (remaining 941 not shown)

  Planarity restraints: 992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 125 "   -0.095 5.00e-02 4.00e+02   1.38e-01 3.03e+01
        pdb=" N   PRO A 126 "    0.238 5.00e-02 4.00e+02
        pdb=" CA  PRO A 126 "   -0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO A 126 "   -0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 125 "    0.095 5.00e-02 4.00e+02   1.38e-01 3.03e+01
        pdb=" N   PRO B 126 "   -0.238 5.00e-02 4.00e+02
        pdb=" CA  PRO B 126 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO B 126 "    0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 290 "   -0.016 2.00e-02 2.50e+03   1.67e-02 4.88e+00
        pdb=" CG  PHE A 290 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 290 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 290 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 290 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 290 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 290 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 989 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 18
        2.18 -     2.86: 2182
        2.86 -     3.54: 8850
        3.54 -     4.22: 13280
        4.22 -     4.90: 22573
  Nonbonded interactions: 46903
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 111 "
            pdb="MG    MG A 503 "
     model   vdw
     1.497 2.170
  nonbonded pdb=" OD1 ASP B 111 "
            pdb="MG    MG B 503 "
     model   vdw
     1.498 2.170
  nonbonded pdb=" OG1 THR B  67 "
            pdb=" CE2 PHE B 131 "
     model   vdw
     1.543 3.340
  nonbonded pdb=" OG1 THR A  67 "
            pdb=" CE2 PHE A 131 "
     model   vdw
     1.543 3.340
  nonbonded pdb=" OD2 ASP A 132 "
            pdb="MG    MG A 502 "
     model   vdw
     1.673 2.170
  ... (remaining 46898 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     27.160
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.093   6066  Z= 0.481
  Angle     :  1.420  23.694   8246  Z= 0.854
  Chirality :  0.062   0.438    944
  Planarity :  0.008   0.138    992
  Dihedral  : 15.614 100.334   2136
  Min Nonbonded Distance : 1.497

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.27 %
    Favored  : 98.41 %
  Cbeta Deviations :  1.46 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.29), residues: 732
  helix:  0.29 (0.22), residues: 488
  sheet:  None (None), residues: 0
  loop : -1.17 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 213 
 HIS   0.016   0.002   HIS B 316 
 PHE   0.039   0.003   PHE A 290 
 TYR   0.023   0.002   TYR B 340 
 ARG   0.003   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14006 (  392)
  hydrogen bonds       : angle       6.41691 ( 1152)
  covalent geometry    : bond        0.00887 ( 6066)
  covalent geometry    : angle       1.41984 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 112
  average time/residue: 0.2147
  time to fit residues: 32.5776
Evaluate side-chains
  94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue  189 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0370
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 133 HIS
A 175 HIS
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 GLN
B 133 HIS
B 175 HIS
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.196422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.156013 restraints weight = 7073.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.161357 restraints weight = 3753.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.164848 restraints weight = 2578.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6066  Z= 0.145
  Angle     :  0.614   7.047   8246  Z= 0.326
  Chirality :  0.040   0.124    944
  Planarity :  0.004   0.033    992
  Dihedral  : 10.561  85.148    872
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.95 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.31), residues: 732
  helix:  1.41 (0.23), residues: 490
  sheet:  None (None), residues: 0
  loop : -1.26 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 176 
 HIS   0.004   0.001   HIS A 316 
 PHE   0.014   0.001   PHE B 165 
 TYR   0.011   0.001   TYR B 340 
 ARG   0.005   0.001   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05148 (  392)
  hydrogen bonds       : angle       4.34972 ( 1152)
  covalent geometry    : bond        0.00311 ( 6066)
  covalent geometry    : angle       0.61373 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.8685 (tp) cc_final: 0.8450 (tp)
REVERT: A  183 MET cc_start: 0.7295 (ptm) cc_final: 0.7009 (ptp)
REVERT: A  345 ILE cc_start: 0.8325 (mt) cc_final: 0.8002 (mt)
REVERT: B  130 LEU cc_start: 0.8687 (tp) cc_final: 0.8450 (tp)
REVERT: B  183 MET cc_start: 0.7286 (ptm) cc_final: 0.7003 (ptp)
REVERT: B  345 ILE cc_start: 0.8318 (mt) cc_final: 0.7994 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2210
  time to fit residues: 32.1953
Evaluate side-chains
  99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.189805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146744 restraints weight = 7169.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.151949 restraints weight = 3971.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155355 restraints weight = 2803.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6066  Z= 0.134
  Angle     :  0.558   7.681   8246  Z= 0.293
  Chirality :  0.039   0.118    944
  Planarity :  0.003   0.028    992
  Dihedral  :  9.640  69.493    870
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.02 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.31), residues: 732
  helix:  1.48 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  56 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.013   0.001   PHE A 290 
 TYR   0.010   0.001   TYR A 172 
 ARG   0.002   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04856 (  392)
  hydrogen bonds       : angle       4.11913 ( 1152)
  covalent geometry    : bond        0.00287 ( 6066)
  covalent geometry    : angle       0.55806 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A  183 MET cc_start: 0.7371 (ptm) cc_final: 0.7121 (ptp)
REVERT: A  292 LYS cc_start: 0.7505 (mtmm) cc_final: 0.7256 (mttp)
REVERT: A  345 ILE cc_start: 0.8382 (mt) cc_final: 0.8047 (mt)
REVERT: B  183 MET cc_start: 0.7370 (ptm) cc_final: 0.7120 (ptp)
REVERT: B  292 LYS cc_start: 0.7502 (mtmm) cc_final: 0.7249 (mttp)
REVERT: B  345 ILE cc_start: 0.8340 (mt) cc_final: 0.7996 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1641
  time to fit residues: 22.8467
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.189092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.145288 restraints weight = 7314.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.150381 restraints weight = 4092.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153507 restraints weight = 2914.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6066  Z= 0.152
  Angle     :  0.556   7.635   8246  Z= 0.293
  Chirality :  0.040   0.126    944
  Planarity :  0.004   0.027    992
  Dihedral  :  9.381  67.907    870
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.51 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.31), residues: 732
  helix:  1.63 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.41 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  56 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.015   0.001   PHE A 290 
 TYR   0.011   0.001   TYR B 172 
 ARG   0.001   0.000   ARG A 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04817 (  392)
  hydrogen bonds       : angle       4.12570 ( 1152)
  covalent geometry    : bond        0.00340 ( 6066)
  covalent geometry    : angle       0.55568 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A  129 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: A  188 LYS cc_start: 0.7621 (mttt) cc_final: 0.6571 (tttm)
REVERT: A  345 ILE cc_start: 0.8336 (mt) cc_final: 0.7992 (mt)
REVERT: B  129 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7676 (mm-30)
REVERT: B  188 LYS cc_start: 0.7627 (mttt) cc_final: 0.6575 (tttm)
REVERT: B  345 ILE cc_start: 0.8327 (mt) cc_final: 0.7980 (mt)
  outliers start: 12
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1556
  time to fit residues: 23.9214
Evaluate side-chains
  115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.175919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129119 restraints weight = 7052.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.133850 restraints weight = 4086.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137026 restraints weight = 2956.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6066  Z= 0.140
  Angle     :  0.539   7.618   8246  Z= 0.284
  Chirality :  0.039   0.122    944
  Planarity :  0.004   0.027    992
  Dihedral  :  9.352  68.474    870
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.67 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.31), residues: 732
  helix:  1.70 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.38 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 213 
 HIS   0.006   0.001   HIS B 316 
 PHE   0.013   0.001   PHE B 165 
 TYR   0.021   0.001   TYR A 340 
 ARG   0.001   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04678 (  392)
  hydrogen bonds       : angle       4.05047 ( 1152)
  covalent geometry    : bond        0.00310 ( 6066)
  covalent geometry    : angle       0.53907 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  188 LYS cc_start: 0.7754 (mttt) cc_final: 0.6743 (tttt)
REVERT: A  290 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7164 (m-10)
REVERT: A  345 ILE cc_start: 0.8415 (mt) cc_final: 0.8058 (mt)
REVERT: B  188 LYS cc_start: 0.7758 (mttt) cc_final: 0.6743 (tttt)
REVERT: B  290 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7159 (m-10)
REVERT: B  345 ILE cc_start: 0.8412 (mt) cc_final: 0.8052 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1307
  time to fit residues: 20.6628
Evaluate side-chains
  118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0270
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.178266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131708 restraints weight = 6968.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.136507 restraints weight = 4055.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139452 restraints weight = 2937.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6066  Z= 0.120
  Angle     :  0.544   8.790   8246  Z= 0.276
  Chirality :  0.039   0.125    944
  Planarity :  0.003   0.029    992
  Dihedral  :  9.232  69.548    870
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.98 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.31), residues: 732
  helix:  1.82 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.39 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 213 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.011   0.001   PHE A 165 
 TYR   0.014   0.001   TYR A 340 
 ARG   0.002   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04461 (  392)
  hydrogen bonds       : angle       3.92247 ( 1152)
  covalent geometry    : bond        0.00254 ( 6066)
  covalent geometry    : angle       0.54414 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A  183 MET cc_start: 0.8000 (pmm) cc_final: 0.7771 (pmm)
REVERT: A  188 LYS cc_start: 0.7687 (mttt) cc_final: 0.6699 (tttt)
REVERT: A  290 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7172 (m-80)
REVERT: A  345 ILE cc_start: 0.8402 (mt) cc_final: 0.8054 (mt)
REVERT: B  183 MET cc_start: 0.7999 (pmm) cc_final: 0.7768 (pmm)
REVERT: B  188 LYS cc_start: 0.7688 (mttt) cc_final: 0.6697 (tttt)
REVERT: B  290 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7169 (m-80)
REVERT: B  345 ILE cc_start: 0.8402 (mt) cc_final: 0.8050 (mt)
  outliers start: 19
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1426
  time to fit residues: 19.6071
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.184609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139471 restraints weight = 7131.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.144212 restraints weight = 4172.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.147280 restraints weight = 3023.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6066  Z= 0.133
  Angle     :  0.563   8.467   8246  Z= 0.287
  Chirality :  0.039   0.126    944
  Planarity :  0.004   0.029    992
  Dihedral  :  9.189  67.839    870
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.78 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 732
  helix:  1.86 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.44 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 213 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.011   0.001   PHE B 165 
 TYR   0.014   0.001   TYR A 340 
 ARG   0.002   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  392)
  hydrogen bonds       : angle       3.95139 ( 1152)
  covalent geometry    : bond        0.00291 ( 6066)
  covalent geometry    : angle       0.56333 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  183 MET cc_start: 0.8074 (pmm) cc_final: 0.7841 (pmm)
REVERT: A  188 LYS cc_start: 0.7648 (mttt) cc_final: 0.6721 (tttt)
REVERT: A  290 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (m-10)
REVERT: A  345 ILE cc_start: 0.8416 (mt) cc_final: 0.8048 (mt)
REVERT: B  183 MET cc_start: 0.8075 (pmm) cc_final: 0.7843 (pmm)
REVERT: B  188 LYS cc_start: 0.7655 (mttt) cc_final: 0.6734 (tttt)
REVERT: B  290 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.7119 (m-10)
REVERT: B  345 ILE cc_start: 0.8382 (mt) cc_final: 0.8044 (mt)
REVERT: B  347 GLU cc_start: 0.8659 (tp30) cc_final: 0.8168 (mm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 104
  average time/residue: 0.1391
  time to fit residues: 20.1098
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0060
   chunk 33 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0050
   chunk 58 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4610

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 GLN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.185826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.140335 restraints weight = 7034.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145131 restraints weight = 4098.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148241 restraints weight = 2971.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6066  Z= 0.120
  Angle     :  0.568   9.187   8246  Z= 0.287
  Chirality :  0.039   0.130    944
  Planarity :  0.004   0.030    992
  Dihedral  :  9.092  68.625    870
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.89 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.31), residues: 732
  helix:  1.89 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.38 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 213 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.009   0.001   PHE A 165 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.002   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  392)
  hydrogen bonds       : angle       3.86464 ( 1152)
  covalent geometry    : bond        0.00256 ( 6066)
  covalent geometry    : angle       0.56801 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A  183 MET cc_start: 0.8040 (pmm) cc_final: 0.7783 (pmm)
REVERT: A  188 LYS cc_start: 0.7547 (mttt) cc_final: 0.6847 (tttt)
REVERT: A  223 LYS cc_start: 0.8359 (tptp) cc_final: 0.7834 (mmmt)
REVERT: A  238 PHE cc_start: 0.8228 (t80) cc_final: 0.7930 (t80)
REVERT: A  290 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7084 (m-10)
REVERT: A  345 ILE cc_start: 0.8324 (mt) cc_final: 0.7987 (mt)
REVERT: B  183 MET cc_start: 0.8045 (pmm) cc_final: 0.7787 (pmm)
REVERT: B  188 LYS cc_start: 0.7566 (mttt) cc_final: 0.6850 (tttt)
REVERT: B  223 LYS cc_start: 0.8383 (tptp) cc_final: 0.7940 (mmmt)
REVERT: B  238 PHE cc_start: 0.8243 (t80) cc_final: 0.7958 (t80)
REVERT: B  290 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7077 (m-10)
REVERT: B  345 ILE cc_start: 0.8320 (mt) cc_final: 0.7981 (mt)
  outliers start: 20
  outliers final: 16
  residues processed: 104
  average time/residue: 0.1549
  time to fit residues: 22.3011
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0040
   chunk 10 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.3390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 GLN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.189157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144027 restraints weight = 7030.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.148949 restraints weight = 4065.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.152197 restraints weight = 2929.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6066  Z= 0.118
  Angle     :  0.577   9.434   8246  Z= 0.288
  Chirality :  0.038   0.121    944
  Planarity :  0.004   0.030    992
  Dihedral  :  9.046  68.591    870
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.00 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.31), residues: 732
  helix:  1.96 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.34 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 213 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.009   0.001   PHE A 161 
 TYR   0.012   0.001   TYR B 172 
 ARG   0.002   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  392)
  hydrogen bonds       : angle       3.78422 ( 1152)
  covalent geometry    : bond        0.00248 ( 6066)
  covalent geometry    : angle       0.57660 ( 8246)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.8022 (pmm) cc_final: 0.7777 (pmm)
REVERT: A  188 LYS cc_start: 0.7493 (mttt) cc_final: 0.6864 (tttt)
REVERT: A  223 LYS cc_start: 0.8365 (tptp) cc_final: 0.7980 (mmmt)
REVERT: A  290 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7155 (m-10)
REVERT: A  345 ILE cc_start: 0.8221 (mt) cc_final: 0.7893 (mt)
REVERT: B  183 MET cc_start: 0.8029 (pmm) cc_final: 0.7780 (pmm)
REVERT: B  188 LYS cc_start: 0.7478 (mttt) cc_final: 0.6865 (tttt)
REVERT: B  223 LYS cc_start: 0.8361 (tptp) cc_final: 0.7965 (mmmt)
REVERT: B  290 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7151 (m-10)
REVERT: B  345 ILE cc_start: 0.8215 (mt) cc_final: 0.7884 (mt)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1461
  time to fit residues: 22.0036
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.181799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135647 restraints weight = 7179.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.140328 restraints weight = 4253.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143264 restraints weight = 3106.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6066  Z= 0.153
  Angle     :  0.631  12.010   8246  Z= 0.310
  Chirality :  0.039   0.121    944
  Planarity :  0.004   0.029    992
  Dihedral  :  9.086  65.772    870
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.95 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.31), residues: 732
  helix:  1.88 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.35 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  56 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.012   0.001   PHE B 290 
 TYR   0.015   0.001   TYR B 340 
 ARG   0.003   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04632 (  392)
  hydrogen bonds       : angle       3.93979 ( 1152)
  covalent geometry    : bond        0.00347 ( 6066)
  covalent geometry    : angle       0.63141 ( 8246)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.8025 (pmm) cc_final: 0.7766 (pmm)
REVERT: A  188 LYS cc_start: 0.7566 (mttt) cc_final: 0.6803 (tttt)
REVERT: A  223 LYS cc_start: 0.8338 (tptp) cc_final: 0.7881 (mmmt)
REVERT: A  290 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7288 (m-10)
REVERT: A  345 ILE cc_start: 0.8385 (mt) cc_final: 0.8037 (mt)
REVERT: B   43 GLU cc_start: 0.8348 (mp0) cc_final: 0.8117 (mp0)
REVERT: B  183 MET cc_start: 0.8029 (pmm) cc_final: 0.7769 (pmm)
REVERT: B  188 LYS cc_start: 0.7518 (mttt) cc_final: 0.6781 (tttt)
REVERT: B  223 LYS cc_start: 0.8250 (tptp) cc_final: 0.7815 (mmmt)
REVERT: B  290 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7283 (m-10)
REVERT: B  345 ILE cc_start: 0.8392 (mt) cc_final: 0.8040 (mt)
  outliers start: 14
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1514
  time to fit residues: 23.9356
Evaluate side-chains
  114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  334 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0970
   chunk 65 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 GLN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.188085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142633 restraints weight = 7192.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147389 restraints weight = 4221.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.150532 restraints weight = 3063.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6066  Z= 0.135
  Angle     :  0.649  13.553   8246  Z= 0.320
  Chirality :  0.039   0.126    944
  Planarity :  0.004   0.035    992
  Dihedral  :  9.026  67.308    870
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.16 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.31), residues: 732
  helix:  1.87 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.36 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  56 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.009   0.001   PHE B 165 
 TYR   0.013   0.001   TYR A 340 
 ARG   0.002   0.000   ARG B  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04518 (  392)
  hydrogen bonds       : angle       3.87708 ( 1152)
  covalent geometry    : bond        0.00301 ( 6066)
  covalent geometry    : angle       0.64854 ( 8246)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2133.56 seconds
wall clock time: 38 minutes 49.50 seconds (2329.50 seconds total)